What good is all that data if you can’t explore it to see what makes you, you!

Common File Types ForGenetic Sequencing Data

FASTQ

FASTQ files are usually fresh off the sequencing machine! They contain raw genetic reads that need to be aligned to a reference genome still. These files generally come in pairs of 2 so you’ll see people reference these files as “paired FASTQ files”. These files are used to make BAM files.

BAM files are made from the process of aligning the FASTQ files to a reference genome. These files are generally very large for human sequence data and contain raw genetic data organized in a way that can really only be understood by specialized software. These files are used to make VCF files.

VCF files contain the actual variants found during the genetic sequencing process. These are the files that most people/labs work with since they are the smaller of the raw data files which makes them easier to work with. Most genetic sequencing labs will provide you with a VCF data file, this is the file that you can use for GeneSavvy’s secondary analysis services such as our Variant Exploration Service or any of our other Health Report Services.

TXT files also usually contain the actual variants found, but they are usually from a genotyping process instead of sequencing. These are usually common files used by ancestry genetic testing companies and are not considered diagnostic grade data. These TXT files also contain variant calls and non-variant calls used for genotyping and common SNP information.

Our Variant Exploration spreadsheet files take the data from VCF or TXT files and organizes it in a way that makes it easier to explore and understand in relation to functional health. Gene names, variant predictions, related health conditions, rarity, and predicted impact are all things we include in our files plus many more. This allows you to explore all the functional aspects of thousands of genetic variants in a much easier way!

Variant Exploration Files VS Report Files

Variant Exploration Files

Our Variant Exploration Files are organized spreadsheets created from the VCF files provided by your genetic sequencing lab. These files will contain information on all of the variants listed in the VCF file you provide (usually ~30,000 variants). We annotate all these variants from data sources that provide useful information related to its function. We also apply our own scoring algorithm which we use to help identify variants with the highest potential impact your health or other traits.

Health Report Files

Our Health Report Files are PDF files that are focused on a subset of genes related to a health topic. These files are generally much easier to follow and will contain actionable suggestions based on the findings within. These reports will help identify genetic patterns related to a specific health topic including genes, variants, and pathways that might not have really been considered before as a causative factor.

The GeneSavvy Bio-Informatic Process

Annotation Databases Used

We use a large amount of 3rd party databases along with our own databases to create useful data related to your variants! Here are some of the data sources you will find in our reports:

GeneFTX

RefSeq

ENSEMBL

dbSNP

ClinVar

OMIM

GWAS

MitoMap

SIFT

PolyPhen2

LRT

MutationTaster

FATHMM

InterVar

CADD

GERP++

ExAC

gnomAD

1000 Genome Project

NCBI

Plus More!

Results You Can Trust

Exome Region Coverage: 50x

Mitochondrial Genome coverage: 500x

GeneSavvy processes your genetic information using state-of-the-art lab equipment and advanced management protocols to ensure the best and most reliable results we can deliver. Our GeneSavvy Genetic testing sequences your genetic exome regions with an average coverage of 50x and your whole mitochondrial genome with an average coverage of 500x.

At GeneSavvy we have developed several proprietary tools that are incorporated in this process to create our full TriarKK™ bioinformatic pipeline.

Treatment Modalities Combined

At GeneSavvy our advisors, panel curators, and treatment option experts have come together from all different modalities of the health industry to provide well rounded treatment options without bias towards one or the other, its all about providing the best action for you. Specialties include: